Curation Projects

Curation projects are thematic, human-authored markdown files under projects/ (e.g. projects/CANCER.md). They track scope, priorities, and progress for a body of related curation work. This page documents the standardized YAML frontmatter that turns a project markdown file into a browsable HTML page with auto-linked entities, and the auto-generated project index.

This is modeled on the project pages in ai4curation/ai-gene-review, adapted to dismech's entity types (diseases, modules, groupings, drugs, phenotypes) rather than genes.

Frontmatter

A project file may begin with a YAML frontmatter block delimited by ---:

---
title: Cancer Curation Project
status: EVERGREEN
description: >-
  Curation of cancers with precise genetic etiology and well-characterized
  pathophysiological progression.
tags: [DISEASE_DOMAIN, ONCOLOGY, FLAGSHIP]
diseases:
  - Lynch_Syndrome
  - Non-Small_Cell_Lung_Cancer
modules:
  - dna_repair_synthetic_lethality
groupings:
  - Mucopolysaccharidoses
drugs:
  - id: CHEBI:45783
    label: imatinib
phenotypes:
  - id: HP:0002664
    label: Neoplasm
---

# Cancer Curation Project
...

All keys are optional; a file with no frontmatter still renders (its title is taken from the first # H1).

Scalar keys

Key	Meaning
`title`	Display title (falls back to the first `# H1`, then the filename).
`status`	One of `PLANNED`, `IN_PROGRESS`, `ACTIVE`, `COMPLETE`, `EVERGREEN`, `ARCHIVED`. Rendered as a colored badge.
`description`	One-line summary shown on the project index card.
`tags`	Free-text labels shown as chips and aggregated on the index.
`nih_topics`	List of `NIHResearchPriorityEnum` keys (e.g. `NIH_HT_89_cellular_quiescence_senescence_cell_death_in`) tagging the NIH Highlighted Funding Topic(s) this project targets. Rendered as blue linked chips to the NIH topic page. See NIH research-priority classification.

Entity keys

Each entity key is a list. List items may be either:

a bare string (the entity token — see the slug convention below), or
a mapping with slug/name/id, an optional label, and an optional note.

Key	Resolves to	Notes
`diseases`	`pages/disorders/<slug>.html`	Token is a disorder slug (the `kb/disorders/*.yaml` stem / disease name).
`modules`	`pages/modules/<stem>.html`	Token is a `kb/modules/` file stem.
`groupings`	`pages/groupings/<slug>.html`	Token is a `Grouping.name` or `kb/groupings/` stem.
`drugs`	external ontology browser	Supply `id:` as a CHEBI/NCIT CURIE for a link.
`phenotypes`	external ontology browser	Supply `id:` as an HP CURIE for a link.

Slug convention and auto-linking

The convention is: refer to diseases (and modules/groupings) by their slug in the markdown body, e.g. write Lynch_Syndrome, not "Lynch Syndrome".

When a project page is rendered, every entity token declared in the frontmatter that resolves to a dismech page is automatically turned into a link wherever it appears in the body — in prose, tables, or lists. Only declared tokens are linked, so there are no spurious links.

Auto-linking deliberately leaves the following untouched:

text inside fenced code blocks and inline `code` spans,
existing markdown links,
filename references such as Lynch_Syndrome.yaml or Lynch_Syndrome.html (a token immediately followed by . is not linked).

The frontmatter also drives the page sidebar, which lists each entity as a chip linking to its page (local entities) or ontology browser (drugs/phenotypes with a CURIE). Tokens that do not resolve render as a muted "unresolved" chip — a quick signal that a slug is mistyped or the entry has not been curated yet.

Rendering

# Render all projects/*.md plus the auto-generated index
just gen-project-pages

# Render a single project page
just gen-project-page projects/CANCER.md

Output goes to pages/projects/ (derived — not committed, like other pages/** HTML). The index at pages/projects/index.html lists every project with its status, tags, and entity counts, and serves as the main project index. just gen-all includes project pages.